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Commits on Aug 13, 2025

• allow low-cov imputation to take either genotype likelihoods or bam files as input

  LindoNkambule

  committed
  75b7f8a

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Commits on Apr 29, 2025

• Merge branch 'main' of https://github.com/atgu/GWASpy

  LindoNkambule

  committed
  f8b9f5e

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• include option to enable/disable running GWAS as part of QC

  LindoNkambule

  committed
  72ee630

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Commits on Mar 25, 2025

• updated argparse ref path in pca.py

  z-koenig

  committed
  506c572

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• updated ref path in pca.py

  z-koenig

  committed
  9e654cf

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Commits on Mar 20, 2025

• updated all instances of HGDP+1kGP ref to public version

  z-koenig

  committed
  f786c35

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• Merge pull request #4 from atgu/zkoenig_update_jointpca_ref

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  z-koenig

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  cd5a5c5

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• updated ref in joint pca to public access path for HGDP+1kGP

  z-koenig

  committed
  66b0112

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Commits on Mar 19, 2025

• unset no_whole_stage_codegen after writing VCF to MT

  LindoNkambule

  committed
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Commits on Feb 5, 2025

• update docs to include GLIMPSE Hail Batch example

  LindoNkambule

  committed
  76fce6c

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• outputs from GLIMPSE2_phase and GLIMPSE2_ligate are automatically indexed

  LindoNkambule

  committed
  c16f68e

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• minor fix for file indexing after running GLIMPSE

  LindoNkambule

  committed
  e369d02

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• fix ref bin output name

  LindoNkambule

  committed
  29b91ea

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• use image with bgzip for extract_ref_sites and properly handle GLIMPSE2 reference bin file output in create_binary_ref

  LindoNkambule

  committed
  21fa520

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• add option to specify chromosomes to run imputation for

  LindoNkambule

  committed
  a2e3364

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Commits on Feb 4, 2025

• add chromosome number to output filename

  LindoNkambule

  committed
  0ff3e08

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Commits on Feb 3, 2025

• index file after fixing

  LindoNkambule

  committed
  4178cc1

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• use correct fixed_file as output

  LindoNkambule

  committed
  c125e58

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• properly declare the stats file as a resource file

  LindoNkambule

  committed
  a25cb94

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Commits on Jan 31, 2025

• replace vcf with ref_fasta when reading reference genome

  LindoNkambule

  committed
  d13b411

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• update docs

  LindoNkambule

  committed
  56163d8

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• declare python requirements required to build the docs

  LindoNkambule

  committed
  3a1d30a

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• add yml file required to build readthedocs

  LindoNkambule

  committed
  e5e161b

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• update docs

  LindoNkambule

  committed
  69459c7

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• remove old files to avoid readthedocs warnings

  LindoNkambule

  committed
  db047c5

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• fix file naming issue

  LindoNkambule

  committed
  6951808

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• add moduel for checking and fixing possible allele flips

  LindoNkambule

  committed
  4ec1e68

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Commits on Jan 30, 2025

• minor updates

  LindoNkambule

  committed
  c7dbf43

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• handle case where all chromosomes are in one file

  LindoNkambule

  committed
  eaa75f0

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• updated docs

  LindoNkambule

  committed
  466046c

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• add option to specify if tags should be added before phasing

  LindoNkambule

  committed
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Commits on Jan 29, 2025

• replace --input-file with --input-vcf for consistency

  LindoNkambule

  committed
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Commits on Jan 28, 2025

• skip plotting if there are no sample annotations in input data

  LindoNkambule

  committed
  bbe90ec

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• avoid using inplace

  LindoNkambule

  committed
  47cbeb6

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• handle multiple VCF formats

  LindoNkambule

  committed
  7e563a8

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